plotSpliceEvent: Plot splice event

In jianhong/ribosomeProfilingQC: Ribosome Profiling Quality Control

Plot splice event

Description

Plot the splice event

Usage

plotSpliceEvent(
  se,
  tx_name,
  coverage,
  group1,
  group2,
  cutoffFDR = 0.05,
  resetIntronWidth = TRUE
)

Arguments

se	Output of spliceEvent
tx_name	Transcript name.
coverage	Coverages of feature region with extensions. Output of coverageDepth
group1, group2	The sample names of group 1 and group 2
cutoffFDR	Cutoff of FDR
resetIntronWidth	logical(1). If set to true, reset the region with no read to minimal width.

Value

A ggplot object.

Examples

## Not run: 
path <- system.file("extdata", package="ribosomeProfilingQC")
RPFs <- dir(path, "RPF.*?\\.[12].bam$", full.names=TRUE)
gtf <- file.path(path, "Danio_rerio.GRCz10.91.chr1.gtf.gz")
coverage <- coverageDepth(RPFs, gtf=gtf, level="gene",
                          region="feature with extension")
group1 <- c("RPF.KD1.1", "RPF.KD1.2")
group2 <- c("RPF.WT.1", "RPF.WT.2")
se <- spliceEvent(coverage, group1, group2)
plotSpliceEvent(se, se$feature[1], coverage, group1, group2)

## End(Not run)

jianhong/ribosomeProfilingQC documentation built on Nov. 3, 2024, 6:33 p.m.